From ea9d6117194944b10ec729b8a1b273cce17a88fd Mon Sep 17 00:00:00 2001 From: Vladimir Buzalka Date: Wed, 3 Jun 2026 07:24:36 +0200 Subject: [PATCH] Migrate IWRS from MySQL to MongoDB - Add IWRS/common/mongo_writer.py with shared connection, indexes, upsert+snapshot helpers - Add IWRS/Patients/import_to_mongo.py (subject_summary + visits) - Add IWRS/Patients/import_notifications_to_mongo.py: parse PDF/JSON directly to Mongo (incl. PDF as BinData), replaces 2-step MySQL flow - Add IWRS/Drugs/import_to_mongo.py (shipments, items, inventory, destruction) - Add IWRS/backfill_mysql_to_mongo.py: one-shot history backfill - Switch IWRS/Patients/run_all.py and IWRS/Drugs/run_all.py to Mongo - Rewrite IWRS/Drugs/create_report.py data loaders to read from Mongo - 8 main collections (upsert = latest state) + 5 snapshot collections (append-only with import_id) under studie database; notifications and destruction are immutable and need no snapshots Co-Authored-By: Claude Opus 4.7 --- IWRS/Drugs/create_report.py | 341 +++++++++--------- IWRS/Drugs/import_to_mongo.py | 253 +++++++++++++ ...3 42847922MDD3003 CZ IWRS overview v1.xlsx | Bin 0 -> 134716 bytes ...3 77242113UCO3001 CZ IWRS overview v1.xlsx | Bin 0 -> 36012 bytes .../shipment_details_101245.xlsx | Bin 0 -> 5526 bytes ...22MDD3003 Subject Summary Report 0622.xlsx | Bin 0 -> 10209 bytes ...2847922MDD3003 Subject Summary Report.xlsx | Bin 0 -> 10209 bytes ...13UCO3001 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-23_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_7_at_site_S10-CZ10008_pk8784.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-23_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_7_at_site_S10-CZ10008_pk8784.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-26_Janssen_42847922MDD3003_Subject_CZ100110003_has_been_screened_at_site_S10-CZ10011.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-26_Janssen_42847922MDD3003_Subject_CZ100110003_has_been_screened_at_site_S10-CZ10011.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-26_Janssen_42847922MDD3003_Subject_CZ100110003_has_been_screened_at_site_S10-CZ10011_pk8952.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-26_Janssen_42847922MDD3003_Subject_CZ100110003_has_been_screened_at_site_S10-CZ10011_pk8952.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-09-29_Janssen_42847922MDD3003_Subject_CZ100120002_has_been_screen_failed_at_site_S10-CZ10012.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-09-29_Janssen_42847922MDD3003_Subject_CZ100120002_has_been_screen_failed_at_site_S10-CZ10012.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-29_Janssen_42847922MDD3003_Subject_CZ100120002_has_been_screen_failed_at_site_S10-CZ10012_pk9146.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-29_Janssen_42847922MDD3003_Subject_CZ100120002_has_been_screen_failed_at_site_S10-CZ10012_pk9146.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk9092.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk9092.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_6_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_6_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_6_at_site_S10-CZ10008_pk9091.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-09-30_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_6_at_site_S10-CZ10008_pk9091.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120003_has_been_screened_at_site_S10-CZ10012.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120003_has_been_screened_at_site_S10-CZ10012.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120003_has_been_screened_at_site_S10-CZ10012_pk9144.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120003_has_been_screened_at_site_S10-CZ10012_pk9144.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120004_has_been_screened_at_site_S10-CZ10012.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120004_has_been_screened_at_site_S10-CZ10012.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120004_has_been_screened_at_site_S10-CZ10012_pk9145.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-01_Janssen_42847922MDD3003_Subject_CZ100120004_has_been_screened_at_site_S10-CZ10012_pk9145.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-03_Janssen_42847922MDD3003_Subject_CZ100040001_Rolled_Over_from_Part_1_into_Part_2_at_site_S10-CZ10004.json (100%) rename 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-07_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10008_pk9415.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-07_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10008_pk9415.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-08_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-08_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.pdf (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-10_Janssen_42847922MDD3003_Subject_CZ100040003_has_been_screened_at_site_S10-CZ10004_pk9644.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-10_Janssen_42847922MDD3003_Subject_CZ100040003_has_been_screened_at_site_S10-CZ10004_pk9644.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-14_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_discontinued_from_IRT_managed_treatment_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-14_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_discontinued_from_IRT_managed_treatment_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-14_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_discontinued_from_IRT_managed_treatment_at_site_S10-CZ10008_pk9821.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-14_Janssen_42847922MDD3003_Subject_CZ100080004_has_been_discontinued_from_IRT_managed_treatment_at_site_S10-CZ10008_pk9821.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100040001_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100040001_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100040001_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004_pk9967.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100040001_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004_pk9967.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100110004_has_been_screen_failed_at_site_S10-CZ10011.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100110004_has_been_screen_failed_at_site_S10-CZ10011.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100110004_has_been_screen_failed_at_site_S10-CZ10011_pk10680.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-17_Janssen_42847922MDD3003_Subject_CZ100110004_has_been_screen_failed_at_site_S10-CZ10011_pk10680.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_dispensing_confirmation_has_occurred_at_site_S10-CZ10004.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_dispensing_confirmation_has_occurred_at_site_S10-CZ10004.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_dispensing_confirmation_has_occurred_at_site_S10-CZ10004_pk10013.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_dispensing_confirmation_has_occurred_at_site_S10-CZ10004_pk10013.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_has_returned_a_medication_at_site_S10-CZ10004.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_has_returned_a_medication_at_site_S10-CZ10004.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_has_returned_a_medication_at_site_S10-CZ10004_pk10012.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-20_Janssen_42847922MDD3003_Subject_CZ100040001_has_returned_a_medication_at_site_S10-CZ10004_pk10012.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-21_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.4_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-21_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.4_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-21_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.4_at_site_S10-CZ10008_pk10103.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-21_Janssen_42847922MDD3003_Subject_CZ100080002_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.4_at_site_S10-CZ10008_pk10103.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk10195.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk10195.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk11621.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100080005_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk11621.pdf (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100110003_randomized_into_Part_1_at_site_S10-CZ10011.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100110003_randomized_into_Part_1_at_site_S10-CZ10011.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100110003_randomized_into_Part_1_at_site_S10-CZ10011_pk10196.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100110003_randomized_into_Part_1_at_site_S10-CZ10011_pk10196.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100120004_randomized_into_Part_1_at_site_S10-CZ10012.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100120004_randomized_into_Part_1_at_site_S10-CZ10012.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100120004_randomized_into_Part_1_at_site_S10-CZ10012_pk10202.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-22_Janssen_42847922MDD3003_Subject_CZ100120004_randomized_into_Part_1_at_site_S10-CZ10012_pk10202.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-24_Janssen_42847922MDD3003_Subject_CZ100080002_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-24_Janssen_42847922MDD3003_Subject_CZ100080002_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-24_Janssen_42847922MDD3003_Subject_CZ100080002_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk10363.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-24_Janssen_42847922MDD3003_Subject_CZ100080002_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk10363.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-29_Janssen_42847922MDD3003_Subject_CZ100080006_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-29_Janssen_42847922MDD3003_Subject_CZ100080006_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.pdf (100%) create mode 100644 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Zpracovano}/2025-10-29_Janssen_42847922MDD3003_Subject_CZ100080006_randomized_into_Part_1_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-29_Janssen_42847922MDD3003_Subject_CZ100080006_randomized_into_Part_1_at_site_S10-CZ10008.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-29_Janssen_42847922MDD3003_Subject_CZ100080006_randomized_into_Part_1_at_site_S10-CZ10008_pk10529.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-10-29_Janssen_42847922MDD3003_Subject_CZ100080006_randomized_into_Part_1_at_site_S10-CZ10008_pk10529.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-10-31_Janssen_42847922MDD3003_Subject_CZ100040001_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.4_at_site_S10-CZ10004.json (100%) rename 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100040001_has_returned_a_medication_at_site_S10-CZ10004_pk10739.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100040001_has_returned_a_medication_at_site_S10-CZ10004_pk10739.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100050002_has_been_screened_at_site_S10-CZ10005.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100050002_has_been_screened_at_site_S10-CZ10005.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100050002_has_been_screened_at_site_S10-CZ10005_pk10759.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100050002_has_been_screened_at_site_S10-CZ10005_pk10759.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100110005_has_been_screened_at_site_S10-CZ10011.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100110005_has_been_screened_at_site_S10-CZ10011.pdf (100%) create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100110005_has_been_screened_at_site_S10-CZ10011_pk10748.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-03_Janssen_42847922MDD3003_Subject_CZ100110005_has_been_screened_at_site_S10-CZ10011_pk10748.pdf rename 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-11_Janssen_42847922MDD3003_Subject_CZ100080006_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk11180.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-11_Janssen_42847922MDD3003_Subject_CZ100080006_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk12802.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-11_Janssen_42847922MDD3003_Subject_CZ100080006_dispensing_confirmation_has_occurred_at_site_S10-CZ10008_pk12802.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-11-11_Janssen_42847922MDD3003_Subject_CZ100080006_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_6_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-21_Janssen_42847922MDD3003_Subject_CZ100110003_has_been_assigned_medication_for_visit_Double_Blind_Part_1_Visit_7_at_site_S10-CZ10011_pk11880.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100040003_dispensing_confirmation_has_occurred_at_site_S10-CZ10004.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100040003_dispensing_confirmation_has_occurred_at_site_S10-CZ10004.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100040003_dispensing_confirmation_has_occurred_at_site_S10-CZ10004_pk11938.json create mode 100644 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100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_dispensing_confirmation_has_occurred_at_site_S10-CZ10011.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_dispensing_confirmation_has_occurred_at_site_S10-CZ10011.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_dispensing_confirmation_has_occurred_at_site_S10-CZ10011_pk11961.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_dispensing_confirmation_has_occurred_at_site_S10-CZ10011_pk11961.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_has_returned_a_medication_at_site_S10-CZ10011.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_has_returned_a_medication_at_site_S10-CZ10011.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_has_returned_a_medication_at_site_S10-CZ10011_pk11966.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-24_Janssen_42847922MDD3003_Subject_CZ100110003_has_returned_a_medication_at_site_S10-CZ10011_pk11966.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-11-25_Janssen_42847922MDD3003_Subject_CZ100080002_has_returned_a_medication_at_site_S10-CZ10008.json (100%) rename 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100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-25_Janssen_42847922MDD3003_Subject_CZ100080006_has_returned_a_medication_at_site_S10-CZ10008_pk12799.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-25_Janssen_42847922MDD3003_Subject_CZ100080006_has_returned_a_medication_at_site_S10-CZ10008_pk12799.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-25_Janssen_42847922MDD3003_Subject_CZ100080006_has_returned_a_medication_at_site_S10-CZ10008_pk13731.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2025-11-25_Janssen_42847922MDD3003_Subject_CZ100080006_has_returned_a_medication_at_site_S10-CZ10008_pk13731.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2025-11-25_Janssen_42847922MDD3003_Subject_CZ100110006_randomized_into_Part_1_at_site_S10-CZ10011.json (100%) rename 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-02-04_Janssen_42847922MDD3003_Subject_CZ100080007_has_returned_a_medication_at_site_S10-CZ10008_pk16133.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-02-04_Janssen_42847922MDD3003_Subject_CZ100080007_has_returned_a_medication_at_site_S10-CZ10008_pk16914.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-02-04_Janssen_42847922MDD3003_Subject_CZ100080007_has_returned_a_medication_at_site_S10-CZ10008_pk16914.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2026-02-06_Janssen_42847922MDD3003_Subject_CZ100040001_has_been_assigned_medication_for_visit_Double_Blind_Maintenance_Visit_3.2_at_site_S10-CZ10004.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100040008_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004_pk21945.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100040008_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004_pk21945.pdf create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100040009_Moved_from_Screening_to_Part_2_at_site_S10-CZ10004.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100040009_Moved_from_Screening_to_Part_2_at_site_S10-CZ10004.pdf create mode 100644 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IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100040009_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004_pk21949.json create mode 100644 IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/Zpracovano/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100040009_has_been_assigned_medication_for_visit_Open_Label_Induction_Visit_1.1_at_site_S10-CZ10004_pk21949.pdf rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100080002_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.json (100%) rename IWRS/Patients/IncomingSourceReportsDetails/42847922MDD3003/{ => Zpracovano}/2026-05-05_Janssen_42847922MDD3003_Subject_CZ100080002_dispensing_confirmation_has_occurred_at_site_S10-CZ10008.pdf (100%) create mode 100644 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claude-memory/project_iwrs_mongo.md diff --git a/IWRS/Drugs/create_report.py b/IWRS/Drugs/create_report.py index 9f3f68e..09eb78b 100644 --- a/IWRS/Drugs/create_report.py +++ b/IWRS/Drugs/create_report.py @@ -1,5 +1,5 @@ import os -import mysql.connector +import sys import pandas as pd from datetime import date from pathlib import Path @@ -7,7 +7,8 @@ from openpyxl import load_workbook from openpyxl.styles import Font, PatternFill, Alignment, Border, Side from openpyxl.utils import get_column_letter -import db_config +sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) +from common.mongo_writer import get_db STUDIES = ["77242113UCO3001", "42847922MDD3003"] @@ -23,70 +24,56 @@ DATE_COLUMNS = { N_SHIP_COLS = 9 # počet shipment sloupců před detail sloupci -# ── DB ──────────────────────────────────────────────────────────────────────── +# ── Načítání dat z MongoDB ──────────────────────────────────────────────────── -def get_conn(): - return mysql.connector.connect( - host=db_config.DB_HOST, port=db_config.DB_PORT, - user=db_config.DB_USER, password=db_config.DB_PASSWORD, - database=db_config.DB_NAME, - ) +INVENTORY_COLS = [ + ("site", "Site"), + ("medication_id", "Med ID"), + ("packaged_lot_no", "Lot No."), + ("original_expiration_date", "Orig Exp Date"), + ("expiration_date", "Exp Date"), + ("received_date", "Rcv Date"), + ("receipt_user", "Rcpt User"), + ("subject_identifier", "Subject ID"), + ("quantity_assigned", "Qty Asgn"), + ("irt_transaction", "IRT Tx"), + ("date_assigned", "Date Asgn"), + ("assignment_user", "Asgn User"), + ("dispensation_status", "Disp Status"), + ("dispensing_date", "Disp Date"), + ("quantity_dispensed", "Qty Disp"), + ("dispensing_user", "Disp User"), + ("quantity_returned", "Qty Ret"), + ("date_returned", "Date Ret"), + ("return_user", "Ret User"), +] -def get_latest_import_id(cursor, study): - cursor.execute( - "SELECT MAX(import_id) AS mid FROM iwrs_import WHERE study=%s AND report_type='drugs'", - (study,), - ) - row = cursor.fetchone() - mid = row["mid"] - if mid is None: - raise RuntimeError(f"Žádná data v MySQL pro studii {study}") - return mid +def load_inventory(study): + db = get_db() + inv = list(db.iwrs_inventory.find({"study": study})) + destr = list(db.iwrs_destruction.find({"study": study})) + # map medication_id -> first basket+date + destr_map = {} + for d in destr: + mid = d.get("medication_id") + if mid and mid not in destr_map: + destr_map[mid] = (d.get("basket_id"), d.get("destruction_date")) + records = [] + for doc in inv: + row = {label: doc.get(key) for key, label in INVENTORY_COLS} + b, dt = destr_map.get(doc.get("medication_id"), (None, None)) + row["Destroyed"] = dt + row["Basket No."] = b + records.append(row) -# ── Načítání dat ────────────────────────────────────────────────────────────── + df = pd.DataFrame(records) + if df.empty: + print(" Inventory: 0 kitu") + return df -def load_inventory(cursor, study, import_id): - sql = """ - SELECT - i.site AS Site, - i.medication_id AS `Med ID`, - i.packaged_lot_no AS `Lot No.`, - i.original_expiration_date AS `Orig Exp Date`, - i.expiration_date AS `Exp Date`, - i.received_date AS `Rcv Date`, - i.receipt_user AS `Rcpt User`, - i.subject_identifier AS `Subject ID`, - i.quantity_assigned AS `Qty Asgn`, - i.irt_transaction AS `IRT Tx`, - i.date_assigned AS `Date Asgn`, - i.assignment_user AS `Asgn User`, - i.dispensation_status AS `Disp Status`, - i.dispensing_date AS `Disp Date`, - i.quantity_dispensed AS `Qty Disp`, - i.dispensing_user AS `Disp User`, - i.quantity_returned AS `Qty Ret`, - i.date_returned AS `Date Ret`, - i.return_user AS `Ret User`, - d.destruction_date AS Destroyed, - d.basket_id AS `Basket No.` - FROM iwrs_inventory i - LEFT JOIN ( - SELECT medication_id, - ANY_VALUE(basket_id) AS basket_id, - ANY_VALUE(destruction_date) AS destruction_date - FROM iwrs_destruction - WHERE study = %s - GROUP BY medication_id - ) d ON d.medication_id = i.medication_id - WHERE i.import_id = %s - AND i.study = %s - ORDER BY i.site, i.received_date, i.medication_id - """ - cursor.execute(sql, (study, import_id, study)) - rows = cursor.fetchall() - df = pd.DataFrame(rows) + df = df.sort_values(["Site", "Rcv Date", "Med ID"], na_position="last").reset_index(drop=True) for col in DATE_COLUMNS: if col in df.columns: df[col] = pd.to_datetime(df[col], errors="coerce") @@ -94,78 +81,102 @@ def load_inventory(cursor, study, import_id): return df -def load_shipments(cursor, study, import_id): - sql = """ - SELECT - s.shipment_id AS `Shipment ID`, - s.status AS `IRT Shipment Status`, - s.type AS Type, - s.ship_from AS `Shipment From`, - s.ship_to_site AS `Ship To:`, - s.request_date AS `Request Date`, - s.received_date AS `Received Date`, - s.received_by AS `Received by`, - s.expected_arrival AS `Expected Arrival`, - i.investigator AS Investigator, - i.medication_description AS `Medication Description`, - i.medication_id AS `Medication ID`, - i.packaged_lot_no AS `Packaged Lot number`, - i.expiration_date AS `Expiration Date`, - i.item_status AS Status - FROM iwrs_shipments s - JOIN iwrs_shipment_items i - ON i.study = s.study - AND i.shipment_id = s.shipment_id - AND i.import_id = %s - WHERE s.import_id = %s - AND s.study = %s - ORDER BY s.ship_to_site, s.shipment_id, i.medication_id - """ - cursor.execute(sql, (import_id, import_id, study)) - rows = cursor.fetchall() - df = pd.DataFrame(rows) +SHIP_COLS = [ + ("shipment_id", "Shipment ID"), + ("status", "IRT Shipment Status"), + ("type", "Type"), + ("ship_from", "Shipment From"), + ("ship_to_site", "Ship To:"), + ("request_date", "Request Date"), + ("received_date", "Received Date"), + ("received_by", "Received by"), + ("expected_arrival", "Expected Arrival"), +] + +ITEM_COLS = [ + ("investigator", "Investigator"), + ("medication_description", "Medication Description"), + ("medication_id", "Medication ID"), + ("packaged_lot_no", "Packaged Lot number"), + ("expiration_date", "Expiration Date"), + ("item_status", "Status"), +] + + +def load_shipments(study): + db = get_db() + ships = list(db.iwrs_shipments.find({"study": study})) + items = list(db.iwrs_shipment_items.find({"study": study})) + + # index items by shipment_id + items_by_ship = {} + for it in items: + items_by_ship.setdefault(it.get("shipment_id"), []).append(it) + + records = [] + for s in ships: + base = {label: s.get(key) for key, label in SHIP_COLS} + for it in items_by_ship.get(s.get("shipment_id"), []): + row = dict(base) + for key, label in ITEM_COLS: + row[label] = it.get(key) + records.append(row) + + df = pd.DataFrame(records) + if df.empty: + print(" Shipments: 0 zásilek, 0 kitu") + return df + + df = df.sort_values(["Ship To:", "Shipment ID", "Medication ID"], na_position="last").reset_index(drop=True) for col in ("Request Date", "Received Date", "Expiration Date", "Expected Arrival"): if col in df.columns: df[col] = pd.to_datetime(df[col], errors="coerce") - n_ship = df["Shipment ID"].nunique() if len(df) else 0 + n_ship = df["Shipment ID"].nunique() print(f" Shipments: {n_ship} zásilek, {len(df)} kitu") return df -def load_visits(cursor, study, import_id): - cursor.execute( - "SELECT MAX(import_id) AS mid FROM iwrs_import WHERE study=%s AND report_type='patients'", - (study,), - ) - patients_import_id = cursor.fetchone()["mid"] or import_id - import_id = patients_import_id - sql = """ - SELECT - v.subject AS Subject, - COALESCE(v.actual_date, v.scheduled_date) AS `Visit Date`, - v.scheduled_date AS `Scheduled Date`, - v.irt_transaction_no AS `IRT Tx No`, - v.irt_transaction_description AS `Visit`, - v.medication_assignment AS `Medication`, - GROUP_CONCAT(v.medication_id ORDER BY v.medication_id SEPARATOR ', ') AS `Med IDs`, - SUM(v.quantity_assigned) AS `Qty` - FROM iwrs_subject_visits v - WHERE v.import_id = %s AND v.study = %s AND v.visit_type = 'Past' - AND v.irt_transaction_no IS NOT NULL - GROUP BY v.subject, v.actual_date, v.scheduled_date, - v.irt_transaction_no, v.irt_transaction_description, v.medication_assignment - ORDER BY v.subject, COALESCE(v.actual_date, v.scheduled_date) - """ - cursor.execute(sql, (import_id, study)) - rows = cursor.fetchall() +def load_visits(study): + db = get_db() + cur = db.iwrs_visits.find({ + "study": study, + "visit_type": "Past", + "irt_transaction_no": {"$ne": None}, + }) + rows = [] + for v in cur: + rows.append({ + "Subject": v.get("subject"), + "Visit Date": v.get("actual_date") or v.get("scheduled_date"), + "Scheduled Date": v.get("scheduled_date"), + "IRT Tx No": v.get("irt_transaction_no"), + "Visit": v.get("irt_transaction_description"), + "Medication": v.get("medication_assignment"), + "medication_id": v.get("medication_id"), + "quantity_assigned": v.get("quantity_assigned"), + }) df = pd.DataFrame(rows) + if df.empty: + print(" Visits: 0 radku") + return df + + # GROUP BY subject/actual/scheduled/irt_no/desc/medication + grouped = ( + df.groupby(["Subject", "Visit Date", "Scheduled Date", "IRT Tx No", "Visit", "Medication"], + dropna=False, as_index=False) + .agg(**{ + "Med IDs": ("medication_id", lambda s: ", ".join(sorted([str(x) for x in s if pd.notna(x)]))), + "Qty": ("quantity_assigned", "sum"), + }) + ) + grouped = grouped.sort_values(["Subject", "Visit Date"]).reset_index(drop=True) for col in ("Visit Date", "Scheduled Date"): - if col in df.columns: - df[col] = pd.to_datetime(df[col], errors="coerce") - if study == "77242113UCO3001" and "Visit" in df.columns: - df["Visit"] = df["Visit"].replace("Subject Number Creation", "Screening") - print(f" Visits: {len(df)} řádků") - return df + if col in grouped.columns: + grouped[col] = pd.to_datetime(grouped[col], errors="coerce") + if study == "77242113UCO3001": + grouped["Visit"] = grouped["Visit"].replace("Subject Number Creation", "Screening") + print(f" Visits: {len(grouped)} řádků") + return grouped # ── Odvozené sheety ─────────────────────────────────────────────────────────── @@ -343,49 +354,42 @@ def format_shipment_sheet(ws, header_color_ship, header_color_detail, n_ship_col # ── Pacienti ───────────────────────────────────────────────────────────────── -PATIENT_TABLE = { - "77242113UCO3001": "iwrs_uco3001_subject_summary", - "42847922MDD3003": "iwrs_mdd3003_subject_summary", -} +def load_patients(study): + db = get_db() + docs = list(db.iwrs_subject_summary.find({"study": study})) + if not docs: + raise RuntimeError(f"Žádná data v Mongo pro pacienty {study}") - -def load_patients(cursor, study): - table = PATIENT_TABLE[study] - cursor.execute(f"SELECT MAX(import_id) AS mid FROM {table}") - mid = cursor.fetchone()["mid"] - if mid is None: - raise RuntimeError(f"Žádná data v MySQL pro pacienty {study}") - extra_cols = "" + base_cols = [ + ("subject", "Subject"), + ("investigator", "Investigator"), + ("age", "Subject's age collection"), + ("cohort_per_irt", "Cohort per IRT"), + ("irt_subject_status", "IRT Subject Status"), + ("last_irt_transaction", "Last Recorded IRT Transaction"), + ("next_irt_transaction", "Next Expected IRT Transaction"), + ("next_irt_transaction_date_local", "Next Expected IRT Transaction Date [Local]"), + ] + uco_extra = [ + ("rescreened_subject", "Rescreened Subject"), + ("adt_ir", "ADT-IR"), + ("three_or_more_advanced_therapies", "3+ Adv. Therapies"), + ("only_oral_5asa_compounds", "Only 5-ASA"), + ("ustekinumab", "Ustekinumab"), + ("isolated_proctitis", "Isolated Proctitis"), + ] + cols = list(base_cols) if study == "77242113UCO3001": - extra_cols = """ - rescreened_subject AS `Rescreened Subject`, - adt_ir AS `ADT-IR`, - three_or_more_advanced_therapies AS `3+ Adv. Therapies`, - only_oral_5asa_compounds AS `Only 5-ASA`, - ustekinumab AS `Ustekinumab`, - isolated_proctitis AS `Isolated Proctitis`,""" - sql = f""" - SELECT - subject AS `Subject`, - investigator AS `Investigator`, - age AS `Subject's age collection`, - cohort_per_irt AS `Cohort per IRT`,{extra_cols} - irt_subject_status AS `IRT Subject Status`, - last_irt_transaction AS `Last Recorded IRT Transaction`, - next_irt_transaction AS `Next Expected IRT Transaction`, - next_irt_transaction_date_local AS `Next Expected IRT Transaction Date [Local]` - FROM {table} - WHERE import_id = %s - ORDER BY subject - """ - cursor.execute(sql, (mid,)) - rows = cursor.fetchall() - df = pd.DataFrame(rows) + cols += uco_extra + + rows = [{label: d.get(key) for key, label in cols} for d in docs] + df = pd.DataFrame(rows).sort_values("Subject").reset_index(drop=True) + if "Next Expected IRT Transaction Date [Local]" in df.columns: df["Next Expected IRT Transaction Date [Local]"] = pd.to_datetime( df["Next Expected IRT Transaction Date [Local]"], errors="coerce" ) - print(f" Pacienti: {len(df)} subjektů (import_id={mid})") + print(f" Pacienti: {len(df)} subjektů") return df @@ -574,18 +578,11 @@ def create_study_report(study): output_file = OUTPUT_DIR / f"{today} {study} CZ IWRS overview v{version}.xlsx" - print(f"\n[{study}] Načítám z MySQL...") - conn = get_conn() - cursor = conn.cursor(dictionary=True) - import_id = get_latest_import_id(cursor, study) - print(f" import_id = {import_id}") - - df = load_inventory(cursor, study, import_id) - shipments_df = load_shipments(cursor, study, import_id) - df_patients = load_patients(cursor, study) - visits_df = load_visits(cursor, study, import_id) - cursor.close() - conn.close() + print(f"\n[{study}] Nacitam z MongoDB...") + df = load_inventory(study) + shipments_df = load_shipments(study) + df_patients = load_patients(study) + visits_df = load_visits(study) expired_df, expired_sheet = build_expired(df) assigned_df = build_assigned_not_dispensed(df) diff --git a/IWRS/Drugs/import_to_mongo.py b/IWRS/Drugs/import_to_mongo.py new file mode 100644 index 0000000..18123b2 --- /dev/null +++ b/IWRS/Drugs/import_to_mongo.py @@ -0,0 +1,253 @@ +""" +Import Drugs dat (shipments, shipment_items, inventory, destruction) z XLSX do MongoDB. + +Volá se z IWRS/Drugs/run_all.py po stažení reportů. +""" + +import os +import sys +import re +import glob + +import pandas as pd + +sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) +from common.mongo_writer import ( + to_str, to_int, to_date, + ensure_indexes, log_import, + bulk_upsert_with_snapshot, bulk_upsert_only, +) + +BASE_DIR = os.path.dirname(os.path.abspath(__file__)) + + +# ── XLSX parsery (převzaté z run_all.py + úprava na Mongo dokumenty) ───────── + +def parse_shipments_report(study): + path = os.path.join(BASE_DIR, f"xls_shipments_{study}", f"shipments_report_{study}.xlsx") + if not os.path.exists(path): + print(f" CHYBI: {path}") + return [] + raw = pd.read_excel(path, header=None) + header_row = None + for i, row in raw.iterrows(): + if "Shipment ID" in [str(v).strip() for v in row]: + header_row = i + break + if header_row is None: + return [] + df = pd.read_excel(path, header=header_row).dropna(how="all") + df = df[df["Location"].astype(str).str.contains("Czech", na=False, case=False)] + col = df.columns.tolist() + rows = [] + for _, r in df.iterrows(): + sid = to_str(r["Shipment ID"]) + if not sid: + continue + rows.append({ + "_id": sid, + "shipment_id": sid, + "study": study, + "status": to_str(r["IRT Shipment Status"]), + "type": to_str(r["Type"]), + "ship_from": to_str(r["Shipment From"]), + "ship_to_site": to_str(r["Ship To:"]), + "location": to_str(r["Location"]), + "request_date": to_date(r["Request Date"]), + "shipped_date": to_date(r["Shipped Date"]), + "received_date": to_date(r["Received Date"]) if "Received Date" in col else None, + "received_by": to_str(r["Received by"]) if "Received by" in col else None, + "delivered_date_utc": to_date(r["Delivered Date [UTC]"]) if "Delivered Date [UTC]" in col else None, + "delivery_recipient": to_str(r["Delivery Recipient"]) if "Delivery Recipient" in col else None, + "delivery_details": to_str(r["Delivery Details"]) if "Delivery Details" in col else None, + "cancelled_date": to_date(r["Cancelled Date"]) if "Cancelled Date" in col else None, + "total_medication_ids": to_int(r["Total Medication IDs"]) if "Total Medication IDs" in col else None, + "tracking_no": to_str(r["Tracking #"]) if "Tracking #" in col else None, + "shipping_category": to_str(r["Shipping Category"]) if "Shipping Category" in col else None, + "expected_arrival": to_date(r["Expected Arrival"]) if "Expected Arrival" in col else None, + }) + return rows + + +def parse_shipment_details(study): + detail_dir = os.path.join(BASE_DIR, f"xls_shipment_details_{study}") + files = sorted(glob.glob(os.path.join(detail_dir, "shipment_details_*.xlsx"))) + rows = [] + for path in files: + m = re.search(r"shipment_details_(.+)\.xlsx", os.path.basename(path)) + shipment_id = m.group(1) if m else "UNKNOWN" + raw = pd.read_excel(path, header=None) + header_row = None + for i, row in raw.iterrows(): + if "Medication ID" in [str(v).strip() for v in row]: + header_row = i + break + if header_row is None: + continue + df = pd.read_excel(path, header=header_row).dropna(how="all") + for _, r in df.iterrows(): + med_desc = (to_str(r.get("Medication Description")) + or to_str(r.get("Medication ID Description"))) + med_type = (to_str(r.get("Medication type")) + or to_str(r.get("Medication ID type"))) + med_id = to_str(r.get("Medication ID")) + if not med_id: + continue + rows.append({ + "_id": f"{shipment_id}:{med_id}", + "study": study, + "shipment_id": shipment_id, + "destination_location": to_str(r.get("Destination Location")), + "shipment_status": to_str(r.get("IRT Shipment Status")), + "shipment_type": to_str(r.get("Type")), + "destination_site": to_str(r.get("Destination Site")), + "investigator": to_str(r.get("Investigator")), + "medication_description": med_desc, + "medication_type": med_type, + "medication_id": med_id, + "packaged_lot_no": to_str(r.get("Packaged Lot number")), + "packaged_lot_description": to_str(r.get("Packaged Lot description")), + "container_id": to_str(r.get("Container ID")), + "quantity": to_int(r.get("Quantity of Medication IDs")), + "expiration_date": to_date(r.get("Expiration Date")), + "item_status": to_str(r.get("Status")), + }) + # dedupe (poslední vyhrává) + by_id = {r["_id"]: r for r in rows} + return list(by_id.values()) + + +def parse_inventory(study): + inv_dir = os.path.join(BASE_DIR, f"xls_reports_{study}") + files = sorted(glob.glob(os.path.join(inv_dir, "onsite_inventory_detail_*.xlsx"))) + rows = [] + for path in files: + raw = pd.read_excel(path, header=None) + site = investigator = location = None + header_row = None + for i, row in raw.iterrows(): + first = str(row.iloc[0]).strip() if pd.notna(row.iloc[0]) else "" + if first.startswith("Site:"): + site = first.replace("Site:", "").strip() + elif first.startswith("Investigator:"): + investigator = first.replace("Investigator:", "").strip() + elif first.startswith("Location:"): + location = first.replace("Location:", "").strip() + if first in ("Medication", "Medication ID") and header_row is None: + header_row = i + if header_row is None: + continue + df = pd.read_excel(path, header=header_row).dropna(how="all") + df = df.rename(columns={df.columns[0]: "medication_id"}) + for _, r in df.iterrows(): + med_id = to_str(r["medication_id"]) + if not med_id or not site: + continue + rows.append({ + "_id": f"{site}:{med_id}", + "study": study, + "site": site, + "investigator": investigator, + "location": location, + "medication_id": med_id, + "packaged_lot_no": to_str(r.get("Packaged Lot number")), + "original_expiration_date": to_date(r.get("Original Expiration Date when Packaged Lot was Added")), + "expiration_date": to_date(r.get("Expiration date")), + "received_date": to_date(r.get("Received Date")), + "receipt_user": to_str(r.get("Shipment Receipt User")), + "subject_identifier": to_str(r.get("Subject Identifier")), + "quantity_assigned": to_int(r.get("Quantity Assigned")), + "irt_transaction": to_str(r.get("IRT Transaction")), + "date_assigned": to_date(r.get("Date Assigned")), + "assignment_user": to_str(r.get("Assignment User")), + "dispensation_status": to_str(r.get("Dispensation Status")), + "dispensing_date": to_date(r.get("Dispensing date") or r.get("Dispensing Date")), + "quantity_dispensed": to_int(r.get("Quantity Dispensed")), + "dispensing_user": to_str(r.get("Dispensing User")), + "quantity_returned": to_int(r.get("Quantity Returned")), + "date_returned": to_date(r.get("Date Returned")), + "return_user": to_str(r.get("Return User")), + }) + by_id = {r["_id"]: r for r in rows} + return list(by_id.values()) + + +def parse_destruction_files(study): + dest_dir = os.path.join(BASE_DIR, f"xls_ip_destruction_{study}") + files = sorted(glob.glob(os.path.join(dest_dir, "ip_destruction_basket_*.xlsx"))) + rows = [] + for path in files: + raw = pd.read_excel(path, header=None) + meta = {} + header_row = None + for i, row in raw.iterrows(): + first = str(row.iloc[0]).strip() if pd.notna(row.iloc[0]) else "" + for key, attr in [ + ("Investigator Name:", "investigator"), + ("Site ID:", "site_id"), + ("Location:", "location"), + ("Basket ID:", "basket_id"), + ("Drug Destruction Created Date:", "destruction_date"), + ]: + if first.startswith(key): + meta[attr] = first.replace(key, "").strip() + if first == "Medication ID Description" and header_row is None: + header_row = i + if header_row is None: + continue + df = pd.read_excel(path, header=header_row).dropna(how="all") + basket_id = meta.get("basket_id") + for _, r in df.iterrows(): + med_id = to_str(r.get("Medication ID")) + if not med_id or not basket_id: + continue + rows.append({ + "_id": f"{basket_id}:{med_id}", + "study": study, + "site_id": meta.get("site_id"), + "investigator": meta.get("investigator"), + "location": meta.get("location"), + "basket_id": basket_id, + "destruction_date": to_date(meta.get("destruction_date")), + "medication_description": to_str(r.get("Medication ID Description")), + "medication_id": med_id, + "packaged_lot_description": to_str(r.get("Packaged Lot description")), + "comments": to_str(r.get("Comments")), + }) + by_id = {r["_id"]: r for r in rows} + return list(by_id.values()) + + +# ── hlavní import ──────────────────────────────────────────────────────────── + +def import_study(study): + print(f"\n [{study}] parsovani XLSX...") + shipments = parse_shipments_report(study) + items = parse_shipment_details(study) + inventory = parse_inventory(study) + destruct = parse_destruction_files(study) + print(f" Zasilky: {len(shipments)} | Polozky: {len(items)} | Sklad: {len(inventory)} | Destrukce: {len(destruct)}") + + import_id = log_import(study, f"drugs_{study}", "drugs", { + "shipments": len(shipments), + "shipment_items": len(items), + "inventory": len(inventory), + "destruction": len(destruct), + }) + print(f" import_id = {import_id}") + + bulk_upsert_with_snapshot("iwrs_shipments", "iwrs_shipments_snapshots", shipments, import_id) + bulk_upsert_with_snapshot("iwrs_shipment_items", "iwrs_shipment_items_snapshots", items, import_id) + bulk_upsert_with_snapshot("iwrs_inventory", "iwrs_inventory_snapshots", inventory, import_id) + bulk_upsert_only("iwrs_destruction", destruct, import_id) + + +def run(studies): + ensure_indexes() + for s in studies: + import_study(s) + + +if __name__ == "__main__": + studies = sys.argv[1:] if len(sys.argv) > 1 else ["77242113UCO3001", "42847922MDD3003"] + run(studies) diff --git a/IWRS/Drugs/output/2026-06-03 42847922MDD3003 CZ IWRS overview v1.xlsx b/IWRS/Drugs/output/2026-06-03 42847922MDD3003 CZ IWRS overview v1.xlsx new file mode 100644 index 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